---
title: "Incidencia coronavirus en Venezuela"
author: "José Alirio Cardoza"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    # social: ["facebook", "twitter", "linkedin"]
    source_code: embed
    vertical_layout: fill
---

```{r setup, include=FALSE}
#------------------ Packages ------------------
library(flexdashboard)
# install.packages("devtools")
# devtools::install_github("RamiKrispin/coronavirus", force = TRUE)
library(coronavirus)
data(coronavirus)
# View(coronavirus)
# max(coronavirus$date)

`%>%` <- magrittr::`%>%`
#------------------ Parameters ------------------
# Set colors
# https://www.w3.org/TR/css-color-3/#svg-color
confirmed_color <- "purple"
active_color <- "#1f77b4"
recovered_color <- "forestgreen"
death_color <- "red"
#------------------ Data ------------------
df <- coronavirus %>%
  # dplyr::filter(date == max(date)) %>%
  dplyr::filter(country == "Venezuela") %>%
  dplyr::group_by(country, type) %>%
  dplyr::summarise(total = sum(cases)) %>%
  tidyr::pivot_wider(
    names_from = type,
    values_from = total
  ) %>%
  # dplyr::mutate(unrecovered = confirmed - ifelse(is.na(recovered), 0, recovered) - ifelse(is.na(death), 0, death)) %>%
  dplyr::mutate(unrecovered = confirmed - ifelse(is.na(death), 0, death)) %>%
  dplyr::arrange(-confirmed) %>%
  dplyr::ungroup() %>%
  dplyr::mutate(country = dplyr::if_else(country == "United Arab Emirates", "UAE", country)) %>%
  dplyr::mutate(country = dplyr::if_else(country == "Mainland China", "China", country)) %>%
  dplyr::mutate(country = dplyr::if_else(country == "North Macedonia", "N.Macedonia", country)) %>%
  dplyr::mutate(country = trimws(country)) %>%
  dplyr::mutate(country = factor(country, levels = country))

df_daily <- coronavirus %>%
  dplyr::filter(country == "Venezuela") %>%
  dplyr::group_by(date, type) %>%
  dplyr::summarise(total = sum(cases, na.rm = TRUE)) %>%
  tidyr::pivot_wider(
    names_from = type,
    values_from = total
  ) %>%
  dplyr::arrange(date) %>%
  dplyr::ungroup() %>%
  #dplyr::mutate(active = confirmed - death - recovered) %>%
  dplyr::mutate(active = confirmed - death) %>%
  dplyr::mutate(
    confirmed_cum = cumsum(confirmed),
    death_cum = cumsum(death),
    # recovered_cum = cumsum(recovered),
    active_cum = cumsum(active)
  )


df1 <- coronavirus %>% dplyr::filter(date == max(date))
```

# Resumen

## Row {data-width="400"}

### confirmed {.value-box}

```{r}

valueBox(
  value = paste(format(sum(df$confirmed), big.mark = ","), "", sep = " "),
  caption = "Contagios totales confirmados",
  icon = "fas fa-user-md",
  color = confirmed_color
)
```

### death {.value-box}

```{r}

valueBox(
  value = paste(format(sum(df$death, na.rm = TRUE), big.mark = ","), " (",
    round(100 * sum(df$death, na.rm = TRUE) / sum(df$confirmed), 1),
    "%)",
    sep = ""
  ),
  caption = "Número total de fallecidos (Tasa de fallecidos)",
  icon = "fas fa-heart-broken",
  color = death_color
)
```

## Row

### **Total de casos acumulados diariamente** (Venezuela)

```{r}
plotly::plot_ly(data = df_daily) %>%
  plotly::add_trace(
    x = ~date,
    # y = ~active_cum,
    y = ~confirmed_cum,
    type = "scatter",
    mode = "lines+markers",
    # name = "Active",
    name = "Contagios",
    line = list(color = active_color),
    marker = list(color = active_color)
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~death_cum,
    type = "scatter",
    mode = "lines+markers",
    name = "Fallecimientos",
    line = list(color = death_color),
    marker = list(color = death_color)
  ) %>%
  # plotly::add_annotations(
  #   x = as.Date("2020-02-04"),
  #   y = 1,
  #   text = paste("First case"),
  #   xref = "x",
  #   yref = "y",
  #   arrowhead = 5,
  #   arrowhead = 3,
  #   arrowsize = 1,
  #   showarrow = TRUE,
  #   ax = -10,
  #   ay = -90
  # ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-26"),
    y = 3,
    text = paste("Primer deceso"),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = 60,
    ay = -90
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-16"),
    y = 14,
    text = paste(
      "Inicio Cuarentena"
    ),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -80,
    ay = -90
  ) %>%
  plotly::layout(
    title = "",
    yaxis = list(title = "Números de casos acumulados"),
    xaxis = list(title = "Fecha"),
    legend = list(x = 0.1, y = 0.9),
    hovermode = "compare"
  )
```

# Tablas comparativas

## Column {data-width="400"}

### **Cantidad de contagios diarios confirmados **

```{r}
daily_confirmed <- coronavirus %>%
  dplyr::filter(type == "confirmed") %>%
  dplyr::filter(date >= "2020-02-29") %>%
  dplyr::mutate(country = country) %>%
  dplyr::group_by(date, country) %>%
  dplyr::summarise(total = sum(cases)) %>%
  dplyr::ungroup() %>%
  tidyr::pivot_wider(names_from = country, values_from = total)

#----------------------------------------
# Plotting the data

daily_confirmed %>%
  plotly::plot_ly() %>%
  plotly::add_trace(
    x = ~date,
    y = ~Venezuela,
    type = "scatter",
    mode = "lines+markers",
    name = "Venezuela"
  ) %>%
  # plotly::add_trace(
  #   x = ~date,
  #   y = ~France,
  #   type = "scatter",
  #   mode = "lines+markers",
  #   name = "France"
  # ) %>%
  # plotly::add_trace(
  #   x = ~date,
  #   y = ~Spain,
  #   type = "scatter",
  #   mode = "lines+markers",
  #   name = "Spain"
  # ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Colombia,
    type = "scatter",
    mode = "lines+markers",
    name = "Colombia"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Brazil,
    type = "scatter",
    mode = "lines+markers",
    name = "Peru"
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~Argentina,
    type = "scatter",
    mode = "lines+markers",
    name = "Argentina"
  ) %>%
  plotly::layout(
    title = "",
    legend = list(x = 0.7, y = 0.9),
    yaxis = list(title = "Número de contagios por fecha"),
    xaxis = list(title = "Fecha"),
    # paper_bgcolor = "black",
    # plot_bgcolor = "black",
    # font = list(color = 'white'),
    hovermode = "compare",
    margin = list(
      # l = 60,
      # r = 40,
      b = 10,
      t = 10,
      pad = 2
    )
  )
```

### **Distribución de casos por tipo**

```{r daily_summary}
df_EU <- coronavirus %>%
  # dplyr::filter(date == max(date)) %>%
  dplyr::filter(country == "Venezuela" |
    country == "Colombia" |
    country == "Peru" |
    country == "Argentina") %>%
  dplyr::group_by(country, type) %>%
  dplyr::summarise(total = sum(cases)) %>%
  tidyr::pivot_wider(
    names_from = type,
    values_from = total
  ) %>%
  # dplyr::mutate(unrecovered = confirmed - ifelse(is.na(recovered), 0, recovered) - ifelse(is.na(death), 0, death)) %>%
  dplyr::mutate(unrecovered = confirmed - ifelse(is.na(death), 0, death)) %>%
  dplyr::arrange(confirmed) %>%
  dplyr::ungroup() %>%
  dplyr::mutate(country = dplyr::if_else(country == "United Arab Emirates", "UAE", country)) %>%
  dplyr::mutate(country = dplyr::if_else(country == "Mainland China", "China", country)) %>%
  dplyr::mutate(country = dplyr::if_else(country == "North Macedonia", "N.Macedonia", country)) %>%
  dplyr::mutate(country = trimws(country)) %>%
  dplyr::mutate(country = factor(country, levels = country))

plotly::plot_ly(
  data = df_EU,
  x = ~country,
  # y = ~unrecovered,
  y = ~ confirmed,
  # text =  ~ confirmed,
  # textposition = 'auto',
  type = "bar",
  name = "Contagios",
  marker = list(color = active_color)
) %>%
  plotly::add_trace(
    y = ~death,
    # text =  ~ death,
    # textposition = 'auto',
    name = "Fallecimientos",
    marker = list(color = death_color)
  ) %>%
  plotly::layout(
    barmode = "stack",
    yaxis = list(title = "Total de contagios y decesos"),
    xaxis = list(title = ""),
    hovermode = "compare",
    margin = list(
      # l = 60,
      # r = 40,
      b = 10,
      t = 10,
      pad = 2
    )
  )
```

# Mapa mundial

### **Comportamiento del COVID-19 resto del mundo** (*use + and - icons to zoom in/out*)

```{r}
# map tab added by Art Steinmetz
library(leaflet)
library(leafpop)
library(purrr)
cv_data_for_plot <- coronavirus %>%
  # dplyr::filter(country == "Venezuela") %>%
  dplyr::filter(cases > 0) %>%
  dplyr::group_by(country, province, lat, long, type) %>%
  dplyr::summarise(cases = sum(cases)) %>%
  dplyr::mutate(log_cases = 2 * log(cases)) %>%
  dplyr::ungroup()
cv_data_for_plot.split <- cv_data_for_plot %>% split(cv_data_for_plot$type)
pal <- colorFactor(c("orange", "red", "green"), domain = c("confirmed", "death", "recovery"))
map_object <- leaflet() %>% addProviderTiles(providers$Stamen.Toner)
names(cv_data_for_plot.split) %>%
  purrr::walk(function(df) {
    map_object <<- map_object %>%
      addCircleMarkers(
        data = cv_data_for_plot.split[[df]],
        lng = ~long, lat = ~lat,
        #                 label=~as.character(cases),
        color = ~ pal(type),
        stroke = FALSE,
        fillOpacity = 0.8,
        radius = ~log_cases,
        popup = leafpop::popupTable(cv_data_for_plot.split[[df]],
          feature.id = FALSE,
          row.numbers = FALSE,
          zcol = c("type", "cases", "country", "province")
        ),
        group = df,
        #                 clusterOptions = markerClusterOptions(removeOutsideVisibleBounds = F),
        labelOptions = labelOptions(
          noHide = F,
          direction = "auto"
        )
      )
  })

map_object %>%
  addLayersControl(
    overlayGroups = names(cv_data_for_plot.split),
    options = layersControlOptions(collapsed = FALSE)
  )
```

# Información

**Tablero Coronavirus: Caso Venezuela**

Este tablero [Tablero Coronavirus: Caso Venezuela] proporciona una visión de los efectos de 2019 Novel Coronavirus COVID-19 (2019-nCoV) epidemia para Venezuela. Este tablero fue construido usando la interfaz de R Markdown y es una adaptación de la información proviniente del tablero [dashboard](https://ramikrispin.github.io/coronavirus_dashboard/){target="_blank"} by Rami Krispin.

**Código**

El código utilizado para la reproducción de este tablero se obtuvo del código publicado por Antoine Soetewey, para mas información dirigirse a la dirección de GitHub: [GitHub](https://github.com/AntoineSoetewey/coronavirus_dashboard){target="_blank"}.

**Datos**

Los datos utilizados para la reproducción de este tablero provienen del conjunto de datos disponibles en el paquete de R [`{coronavirus}`](https://github.com/RamiKrispin/coronavirus){target="_blank"}. Asegurar de descargar la versión en desarrollo para obtener la ultima version disponibles de los datos:

    install.packages("devtools")
    devtools::install_github("RamiKrispin/coronavirus")

Los datos primarios o sin procesar provienen de:

Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus [repository](https://github.com/RamiKrispin/coronavirus-csv){target="_blank"}.

**Información**

Para mayor información acerca de como reproducir este tablero dirigirse al artículo  publicado por el autor del código ; [article](https://statsandr.com/blog/how-to-create-a-simple-coronavirus-dashboard-specific-to-your-country-in-r/).

**Actualización**

La ultima versión disponible de los datos tienen fecha `r format(max(coronavirus$date), "%A %B %d, %Y")` y este tablero fue actualizado `r format(Sys.time(), "%A %B %d, %Y")`.

*Dirigirse [statsandr.com](https://statsandr.com/) (blog del autor del código) ó [antoinesoetewey.com](https://www.antoinesoetewey.com/) (website del autor del código)*.